EMBOSS: Project Meeting (Mon 21st January 2002)


HGMP: Alan Bleasby, Damian Counsel, Jon Ison, Gary Williams, Lisa Mullan, Waqas Awan, Tim Carver, Hugh Morgan, Ranjeeva Ranasinghe
Lion: Peter Rice, Thomas Laurent, Bijay Jassal
EBI: Rodrigo Lopez, Vincent Lombard, Nicola Harte, Adam Lowe

1. Matters Arising

: ) Welcome, new faces ! : )

Alan reported that EMBOSS 2.1.0 was released on Christmas Eve. The whole library had been checked for memory leaks. EMBOSS 2.2.0 was released last week and corrected a few bugs in 2.1.0. Apple have agreed to ship a machine running MacOSX for an initial 3 month evaluation period. IBM have loaned the EMBOSS team a 4-processor machine running AIX 4.3.3 for 3 years for porting purposes. He has written an application called biosed to delete specific patterns from a sequence. He has modified the library to read Stockholm (PFAM) format files; the code will cope with discrete files but is not appropriate for indexing purposes. He has modified dotup and dotmatcher to take a -stretch option forcing each axis to cover the screen. He is working on EMBL processing and nightly updates processing.

Damian is working on training materials for an advanced EMBOSS course ("Biocobbler") to include scripting in EMBOSS.

Jon has modified coorde for parsing of secondary structure and "heterogens" and will commit a working version soon. He has been working with Ranjeeva and Waqas on their applications.

Gary is doing a major overhaul of the online documentation including documenting individual "themes" in EMBOSS. He has committed the primer3 application which is a wrapper to primer3, and the listor application for list file manipulation.

Lisa reported that she is attending a Java course to enable her to develop a help system to JEMBOSS. She is planning to use Ranjeeva and Jon's applications on two forthcoming courses.

Waqas is still working with Jon on the "funky" application - for the generation of a database of functional sites in protein structures from residue contact information.

Tim has been fixing bugs in JEMBOSS. He has been writing documentation for setting up JEMBOSS servers.

Hugh has been evaluating meta languages (esp XML and X3D) to interface EMBOSS applications and GUI's such as JEMBOSS.

Ranjeeva has committed seqsort (for processing the results of psiblast and swissprot searches for SCOP families)and an application called seqnr (for removing redundancy from seqsort output). He has committed the applications alignwrap (a wrapper to clustalw for extending seed alignments with a set of sequences).

Thomas reported that he has integrated the first 14 requested applications and is waiting for feedback, and is working on generating ACD sections to improve the organization of ACD files.

Bijay has been writing parsers (3) for parsing the output of EMBOSS applications (10).

Peter reported on his work on alignment and report formats. He has done a quality test sweep on the applications. He is working on integration of est2genome and einverted into SRS.

2. A.O.B.

3. Date Of Next Meeting

Next meeting to be held at 10.00 on Friday 1st February, HGMP